Table 1 The optimized 1st order Markov chains for TFBS. The optimized arrangement of dependent positions within TFBS for the 1st order Markov model. N and N D are total number of motif positions and the number of positions significantly dependent, respectively.
From: Optimized mixed Markov models for motif identification
ID# | Name | N | N D | Position order |
|---|---|---|---|---|
1 | V$AP1_Q4_01 | 8 | 8 | 7-3-1-2-0-6-5-4 |
2 | V$AP1_Q6_01 | 9 | 8 | 2-3-1-4-5-7-8-6 |
3 | V$AP1_Q2_01 | 12 | 9 | 4-3-5-6-7-10-11-9-1 |
4 | V$CDPCR1_01 | 10 | 9 | 3-4-2-9-6-5-7-8-1 |
5 | V$ATF_01 | 14 | 8 | 1-0-10-9-11-2-13-12 |
6 | V$CHOP_01 | 13 | 10 | 5-4-6-7-9-10-0-8-11-12 |
7 | V$CDPCR3_01 | 15 | 10 | 3-0-1-8-9-13-4-6-2-5 |
8 | V$CDPCR3HD_01 | 10 | 5 | 1-8-9-2-7 |
9 | V$CREB_Q2_01 | 14 | 8 | 1-11-12-0-2-3-9-8 |
10 | V$CREB_Q4_01 | 11 | 6 | 7-6-1-8-9-10 |
11 | V$CREB_Q3 | 6 | 4 | 4-5-1-0 |
12 | V$CEBP_Q3 | 12 | 9 | 8-9-5-6-4-11-3-2-10 |
13 | V$CEBPB_01 | 14 | 4 | 0-13-11-3 |
14 | V$E2F_Q4_01 | 11 | 4 | 1-8-7-0 |
15 | V$E2F_Q6_01 | 12 | 8 | 8-3-7-0-2-11-9-10 |
16 | V$E2F1DP1_01 | 8 | 5 | 3-4-0-6-7 |
17 | V$E2F1DP2_01 | 8 | 5 | 5-6-7-3-4 |
18 | V$E2F4DP1_01 | 8 | 4 | 3-4-0-1 |
19 | V$E2F4DP2_01 | 8 | 5 | 4-3-7-1-0 |
20 | V$ETS_Q4 | 12 | 8 | 11-2-5-10-4-3-0-1 |
21 | V$ELK1_02 | 14 | 4 | 10-11-2-3 |
22 | V$FAC1_01 | 14 | 12 | 12-6-10-11-13-4-9-8-5-1-0-7 |
23 | V$FOXD3_01 | 12 | 11 | 1-3-8-7-9-10-11-2-0-4-6 |
24 | V$FOXO1_02 | 14 | 11 | 8-9-10-12-7-6-2-0-11-1-3 |
25 | V$HNF4_Q6 | 9 | 7 | 4-3-2-6-8-1-7 |
26 | V$HNF1_Q6 | 18 | 15 | 3-11-12-1-4-8-13-5-9-0-6-16-14-2-10 |
27 | V$HNF3_Q6 | 13 | 11 | 1-10-7-5-3-4-12-9-0-2-8 |
28 | V$E2F1DP1RB_01 | 8 | 5 | 1-7-3-0-4 |
29 | V$IRF7_01 | 18 | 13 | 3-2-0-16-15-17-1-7-6-8-14-9-12 |
30 | V$LUN1_01 | 17 | 8 | 8-9-10-7-12-11-14-13 |
31 | V$MZF1_01 | 8 | 4 | 0-1-4-5 |
32 | V$MYC_Q2 | 7 | 4 | 4-5-3-1 |
33 | V$NFAT_Q4_01 | 10 | 4 | 6-8-9-5 |
34 | V$NFKAPPAB_01 | 10 | 4 | 5-7-9-2 |
35 | V$NKX22_01 | 10 | 6 | 9-8-6-1-0-7 |
36 | V$OCT_Q6 | 11 | 10 | 8-2-0-10-5-3-9-6-4-7 |
37 | V$PAX_Q6 | 11 | 10 | 10-6-7-0-9-3-1-5-4-2 |
38 | V$PAX6_01 | 21 | 21 | 15-17-16-18-6-8-19-13-11-3-2-1-0-20-7-10-4-9-5-14-12 |
39 | V$PBX1_02 | 15 | 10 | 6-12-2-0-3-1-11-13-14-4 |
40 | V$RSRFC4_Q2 | 17 | 6 | 6-7-0-13-2-3 |
41 | V$RSRFC4_01 | 16 | 8 | 6-7-9-1-2-13-12-8 |
42 | V$STAT5A_01 | 15 | 7 | 8-12-1-13-0-4-5 |
43 | V$SOX9_B1 | 14 | 9 | 1-13-0-2-11-5-3-10-4 |
44 | V$SRY_01 | 7 | 4 | 4-6-0-1 |
45 | V$SRY_02 | 12 | 4 | 1-3-11-4 |
46 | V$STAT5A_02 | 24 | 16 | 7-12-20-15-16-17-18-19-22-1-21-13-5-6-9-23 |
47 | V$SP1_Q2_01 | 10 | 7 | 7-3-8-0-4-9-5 |
48 | V$SP1_Q4_01 | 13 | 13 | 0-2-11-12-6-1-3-10-9-8-7-4-5 |
49 | V$SP1_Q6_01 | 10 | 10 | 3-5-8-9-0-7-4-2-6-1 |
50 | V$USF_Q6_01 | 12 | 8 | 3-11-4-5-7-2-1-8 |
51 | V$XBP1_01 | 17 | 9 | 13-5-3-4-15-11-10-12-0 |
52 | V$ZID_01 | 13 | 8 | 6-7-4-8-12-10-9-11 |
53 | I$DRI_01 | 10 | 7 | 6-9-8-7-0-1-2 |